Implementation and testing of an automated EST processing and similarity analysis system

Expressed sequence tag (EST) sequencing projects are being undertaken in an effort to identify the function of as many genes as possible from entire genomes. Putative function can be determined by analyzing the similarity of the ESTs to sequences in the public databases. We are involved in a long-term project to research and develop database technology to store and analyze ESTs for Arabidopsis thaliana. The massive amounts of ESTs being produced through automated sequencing technologies necessitates the automated processing and similarity analysis of the ESTs. This paper describes a complete software system that takes ESTs from a sequencing machine, analyzes them for quality, and searches in public databases of previously known sequences. Automating the processing and analysis of the several thousand ESTs produced to date by the Michigan State University, Arabidopsis cDNA Sequencing Project has improved the quality of the EST data and the speed at which ESTs can be entered in the public databases